Browsing by Subject "cancer"

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  • Vakkilainen, Svetlana; Taskinen, Mervi; Klemetti, Paula; Pukkala, Eero; Mäkitie, Outi (2019)
    Cartilage-hair hypoplasia (CHH) is a skeletal dysplasia with combined immunodeficiency, variable clinical course and increased risk of malignancy. Management of CHH is complicated by a paucity of long-term follow-up data, as well as knowledge on prognostic factors. We assessed clinical course and risk factors for mortality in a prospective cohort study of 80 patients with CHH recruited in 1985-1991 and followed up until 2016. For all patients we collected additional health information from health records and from the national Medical Databases and Cause-of-death Registry. The primary outcome was immunodeficiency-related death, including death from infections, lung disease and malignancy. Standardized mortality ratios (SMRs) were calculated using national mortality rates as reference. Half of the patients (57%, n = 46) manifested no symptoms of immunodeficiency during follow-up while 19% (n = 15) and 24% (n = 19) demonstrated symptoms of humoral or combined immunodeficiency, including six cases of adult-onset immunodeficiency. In a significant proportion of patients (17/79, 22%), clinical features of immunodeficiency progressed over time. Of the 15 patients with non-skin cancer, eight had no preceding clinical symptoms of immunodeficiency. Altogether 20 patients had deceased (SMR = 7.0, 95% CI = 4.3-11); most commonly from malignancy (n = 7, SMR = 10, 95% CI = 4.1-21) and lung disease (n = 4, SMR = 46, 95% CI = 9.5-130). Mortality associated with birth length below-4 standard deviation (compared to normal, SMR/SMR ratio = 5.4, 95% CI = 1.5-20), symptoms of combined immunodeficiency (compared to asymptomatic, SMR/SMR ratio= 3.9, 95% CI = 1.3-11), Hirschsprung disease (odds ratio (OR) 7.2, 95% CI = 1.04-55), pneumonia in the first year of life or recurrently in adulthood (OR = 7.6/19, 95% CI = 1.3-43/2.6-140) and autoimmunity in adulthood (OR = 39, 95% CI = 3.5-430). In conclusion, patients with CHH may develop adult-onset immunodeficiency or malignancy without preceding clinical symptoms of immune defect, warranting careful follow-up. Variable disease course and risk factors for mortality should be acknowledged.
  • Van Der Wel, Kjetil A.; Östergren, Olof; Lundberg, Olle; Korhonen, Kaarina; Martikainen, Pekka; Andersen, Anne-Marie Nybo; Urhoj, Stine Kjaer (2019)
    Aims: Future research on health inequality relies on data that cover life-course exposure, different birth cohorts and variation in policy contexts. Nordic register data have long been celebrated as a ?gold mine? for research, and fulfil many of these criteria. However, access to and use of such data are hampered by a number of hurdles and bottlenecks. We present and discuss the experiences of an ongoing Nordic consortium from the process of acquiring register data on socio-economic conditions and health in Denmark, Finland, Norway and Sweden. Methods: We compare experiences of data-acquisition processes from a researcher?s perspective in the four countries and discuss the comparability of register data and the modes of collaboration available to researchers, given the prevailing ethical and legal restrictions. Results: The application processes we experienced were time-consuming, and decision structures were often fragmented. We found substantial variation between the countries in terms of processing times, costs and the administrative burden of the researcher. Concerned agencies differed in policy and practice which influenced both how and when data were delivered. These discrepancies present a challenge to comparative research. Conclusions: We conclude that there are few signs of harmonisation, as called for by previous policy documents and research papers. Ethical vetting needs to be centralised both within and between countries in order to improve data access. Institutional factors that seem to facilitate access to register data at the national level include single storage environments for health and social data, simplified ethical vetting and user guidance.
  • Ahlberg, Sara; Grace, Delia; Kiarie, Gideon; Kirino, Yumi; Lindahl, Johanna (2018)
    Aflatoxin M1 (AFM1), a human carcinogen, is found in milk products and may have potentially severe health impacts on milk consumers. We assessed the risk of cancer and stunting as a result of AFM1 consumption in Nairobi, Kenya, using worst case assumptions of toxicity and data from previous studies. Almost all (99.5%) milk was contaminated with AFM1. Cancer risk caused by AFM1 was lower among consumers purchasing from formal markets (0.003 cases per 100,000) than for low-income consumers (0.006 cases per 100,000) purchasing from informal markets. Overall cancer risk (0.004 cases per 100,000) from AFM1 alone was low. Stunting is multifactorial, but assuming only AFM1 consumption was the determinant, consumption of milk contaminated with AFM1 levels found in this study could contribute to 2.1% of children below three years in middle-income families, and 2.4% in low-income families, being stunted. Overall, 2.7% of children could hypothetically be stunted due to AFM1 exposure from milk. Based on our results AFM1 levels found in milk could contribute to an average of −0.340 height for age z-score reduction in growth. The exposure to AFM1 from milk is 46 ng/day on average, but children bear higher exposure of 3.5 ng/kg bodyweight (bw)/day compared to adults, at 0.8 ng/kg bw/day. Our paper shows that concern over aflatoxins in milk in Nairobi is disproportionate if only risk of cancer is considered, but that the effect on stunting children might be much more significant from a public health perspective; however, there is still insufficient data on the health effects of AFM1.
  • Allan, Robert (Edinburgh, 1821)
  • Mascitti, Marco; Zhurakivska, Khrystyna; Togni, Lucrezia; Caponio, Vito C. A.; Almangush, Alhadi; Balercia, Paolo; Balercia, Andrea; Rubini, Corrado; Lo Muzio, Lorenzo; Santarelli, Andrea; Troiano, Giuseppe (2020)
    Aims One of the objectives of current research is to customise the treatment of cancer patients. The achievement of this objective requires stratification of patients based on the most significant prognostic factors. The aims of this study were to evaluate the prognostic value of the tumour-stroma ratio (TSR), defined as the proportion of tumour cells relative to surrounding stroma, in patients with oral tongue squamous cell carcinoma (OTSCC), and to develop a prognostic nomogram based on the most significant clinicopathological features. Methods and results Clinicopathological data of 211 patients treated at 'Ospedali Riuniti' General Hospital (Ancona, Italy) for OTSCC were collected. One hundred and thirty-nine patients were restaged according to the 8th edition American Joint Committee on Cancer (AJCC) staging system. Evaluation of the TSR was performed on haematoxylin and eosin-stained slides, and correlation with survival outcomes was evaluated. In addition, with the aim of integrating the independent value of the TSR with the 8th edition AJCC staging system, a prognostic nomogram for OTSCC has been developed. OTSCC with a low TSR (i.e. a high proportion of stroma and a low proportion of tumour cells) was shown to have negative prognostic value in terms of disease-specific survival, with a hazard ratio (HR) of 1.883 and a 95% confidence interval (CI) of 1.033-3.432 (P = 0.039), and overall survival (HR = 1.747, 95% CI 0.967-3.154;P = 0.044), independently of other histological and clinical parameters. For the cohort of 139 patients restaged according to the 8th edition AJCC staging system, variables correlating with a poor prognosis were: the TSR, perineural invasion, and sex. The nomogram built on these parameters showed good predictive capacity, outperforming the 8th edition AJCC staging system in stratifying disease-specific survival in OTSCC patients. Conclusions Including the TSR in the predictive model could improve risk stratification of OTSCC patients and aid in making treatment decisions.
  • Bokharaie, Honey; Kolch, Walter; Krstic, Aleksandar (2022)
    Alternative splicing (AS) is one of the hallmarks of human cancer. One of the most common mechanisms of vemurafenib resistance in malignant melanoma is AS of BRAF, occurring in 15-30% of patients. The aim of our study was to investigate the transcriptome and AS D04landscape in the isogenic BRAF V600E cell line pair SK-MEL-239, where the vemurafenib-resistant derivative expresses a truncated BRAF transcript that lacks the RAS-binding domain. Transcriptome analysis showed differential expression of spliceosome components between the two cell lines. AS analysis, by four different tools, DEXSeq, rMATS, ASpli, and LeafCutter, has identified genes enriched for cell motility and melanin synthesis in vemurafenib-resistant cells. Overlapping predictions for all four tools have been experimentally validated. Our study expands the understanding of melanoma drug resistance from a new perspective and supports the need to investigate in detail the aberrant AS landscape in patients with malignant melanoma. Alternative mRNA splicing is common in cancers. In BRAF V600E-mutated malignant melanoma, a frequent mechanism of acquired resistance to BRAF inhibitors involves alternative splicing (AS) of BRAF. The resulting shortened BRAF protein constitutively dimerizes and conveys drug resistance. Here, we have analysed AS in SK-MEL-239 melanoma cells and a BRAF inhibitor (vemurafenib)-resistant derivative that expresses an AS, shortened BRAF V600E transcript. Transcriptome analysis showed differential expression of spliceosome components between the two cell lines. As there is no consensus approach to analysing AS events, we used and compared four common AS softwares based on different principles, DEXSeq, rMATS, ASpli, and LeafCutter. Two of them correctly identified the BRAF V600E AS in the vemurafenib-resistant cells. Only 12 AS events were identified by all four softwares. Testing the AS predictions experimentally showed that these overlapping predictions are highly accurate. Interestingly, they identified AS caused alterations in the expression of melanin synthesis and cell migration genes in the vemurafenib-resistant cells. This analysis shows that combining different AS analysis approaches produces reliable results and meaningful, biologically testable hypotheses.
  • Sanikini, Harinakshi; Muller, David C; Sophiea, Marisa; Rinaldi, Sabina; Agudo, Antonio; Duell, Eric J; Weiderpass, Elisabete; Overvad, Kim; Tjønneland, Anne; Halkjær, Jytte; Boutron-Ruault, Marie-Christine; Carbonnel, Franck; Cervenka, Iris; Boeing, Heiner; Kaaks, Rudolf; Kühn, Tilman; Trichopoulou, Antonia; Martimianaki, Georgia; Karakatsani, Anna; Pala, Valeria; Palli, Domenico; Mattiello, Amalia; Tumino, Rosario; Sacerdote, Carlotta; Skeie, Guri; Rylander, Charlotta; López, María Dolores Chirlaque; Sánchez, Maria-Jose; Ardanaz, Eva; Regnér, Sara; Stocks, Tanja; Bueno-de-Mesquita, Bas; Vermeulen, Roel C.H.; Aune, Dagfinn; Tong, Tammy Y.N.; Kliemann, Nathalie; Murphy, Neil; Chadeau-Hyam, Marc; Gunter, Marc J; Cross, Amanda J (2020)
    Obesity has been associated with upper gastrointestinal cancers; however, there are limited prospective data on associations by subtype/subsite. Obesity can impact hormonal factors, which have been hypothesized to play a role in these cancers. We investigated anthropometric and reproductive factors in relation to esophageal and gastric cancer by subtype and subsite for 476,160 participants from the European Prospective Investigation into Cancer and Nutrition cohort. Multivariable hazard ratios (HRs) and 95%-confidence intervals (CIs) were estimated using Cox models. During a mean follow-up of 14 years, 220 esophageal adenocarcinomas (EA), 195 esophageal squamous cell carcinomas, 243 gastric cardia (GC) and 373 gastric non-cardia (GNC) cancers were diagnosed. Body mass index (BMI) was associated with EA in men (BMI≥30 vs 18.5-25kg/m2: HR=1.94, 95%-CI: 1.25-3.03) and women (HR=2.66, 95%-CI: 1.15-6.19); however, adjustment for waist-to-hip ratio (WHR) attenuated these associations. WHR and waist circumference (WC) were associated with EA in men (HR=3.47, 95%-CI: 1.99-6.06 for WHR >0.96 vs 98 vs 0.82 vs 83 vs 2 vs 0) and age at first pregnancy and GNC (HR=0.54, 95%-CI: 0.32-0.91; >26 vs
  • Chandola, Chetan; Kalme, Sheetal; Casteleijn, Marco G.; Urtti, Arto; Neerathilingam, Muniasamy (2016)
    Aptamers are small, single-stranded oligonucleotides (DNA or RNA) that bind to their target with high specificity and affinity. Although aptamers are analogous to antibodies for a wide range of target recognition and variety of applications, they have significant advantages over antibodies. Since aptamers have recently emerged as a class of biomolecules with an application in a wide array of fields, we need to summarize the latest developments herein. In this review we will discuss about the latest developments in using aptamers in diagnostics, drug delivery and imaging. We begin with diagnostics, discussing the application of aptamers for the detection of infective agents itself, antigens/toxins (bacteria), biomarkers (cancer), or a combination. The ease of conjugation and labelling of aptamers makes them a potential tool for diagnostics. Also, due to the reduced off-target effects of aptamers, their use as a potential drug delivery tool is emerging rapidly. Hence, we discuss their use in targeted delivery in conjugation with siRNAs, nanoparticles, liposomes, drugs and antibodies. Finally, we discuss about the conjugation strategies applicable for RNA and DNA aptamers for imaging. Their stability and self-assembly after heating makes them superior over protein-based binding molecules in terms of labelling and conjugation strategies.
  • Trabulo, Carolina; Lopes, Joana; Dias, David da Silva; Gramaca, Joao; Fernandes, Isabel; Gameiro, Rita; Pina, Idilia; Mäkitie, Antti; Ottery, Faith; Ravasco, Paula (2022)
    BackgroundNutritional status in patients with cancer has a determining role in the evolution of the disease and tolerance to treatments. Severity of undernutrition impacts morbidity and mortality in cancer patients and can limit patient response to the optimal therapies if nutritional issues are not appropriately addressed and managed. Despite the importance of malnutrition for the clinical evolution of oncology patients, there is not yet a universally accepted standard method for evaluating malnutrition in such patients. The aim of this study was to stratify the nutritional status of inpatients at an Oncology Department. MethodsThis is an observational study with 561 cancer patients, assessed at admission to a Medical Oncology Department from November 2016 to February 2020. All patients were considered eligible. Non-compliant and/or comatose patients were excluded. Nutritional status was assessed using the PG-SGA, BMI classified with the WHO criteria, and calculation of the percentage of weight loss in the previous 3-6 months. ResultsA total of 561 patients (303 F: 258 M; mean age 65 +/- 13 years) were included. One-third of the patients, n=191/561 (34%), lost 6% of their weight in the month prior to admission and 297/561 (53%) patients lost 10.2% of weight in the previous 6 months. Mean BMI was 24.1 +/- 5.8 kg/m(2); N = 280/561 (50%) patients had regular BMI according to the WHO criteria. N = 331/561 (59%) patients reported eating less in the month prior to admission. N = 303/561 (54%) had moderate/severe deficits of muscle and adipose compartments. The PG-SGA identified 499/561 (89%) patients as moderately/severely malnourished, of which 466/561 (83%) patients scored >= 9 points, meeting criteria for a critical need for nutritional support. Fifteen percent of patients scored >4 points, indicating a need for directed therapy for symptom control and only 1% scored
  • Eskelinen, Eeva-Liisa (2019)
    Autophagy is a conserved catabolic process that delivers cytoplasmic components and organelles to lysosomes for degradation and recycling. This pathway serves to degrade nonfunctional organelles and aggregate-prone proteins, as well as to produce substrates for energy production and biosynthesis. Autophagy is especially important for the maintenance of stem cells, and for the survival and homeostasis of post-mitotic cells like neurons. Functional autophagy promotes longevity in several model organisms. Autophagy regulates immunity and inflammation at several levels and has both anti- and pro-tumorigenic roles in cancer. This review provides a concise overview of autophagy and its importance in cellular and organismal homeostasis, with emphasis on aging, stem cells, neuronal cells, immunity, inflammation, and cancer.
  • Amatya, Sajeen Bahadur; Salmi, Sonja; Kainulainen, Veera; Karihtala, Peeter; Reunanen, Justus (2021)
    Simple Summary:& nbsp;Microbial dysbiosis has been credited as one of the contributing factors to the development and progression of gastrointestinal tract cancer. The altered microbiota influences carcinogenesis through the induction of instability and damage to genetic material, modulation of host metabolic and inflammatory pathways, production of carcinogenic metabolites, and suppression of host antitumor response. These microbes secrete extracellular vesicles that are possibly carrying carcinogenic bioactive metabolites within their cargo. Studies have illustrated the ability of bacterial extracellular vesicles to cross the intestinal epithelial barrier and selectively accumulate near intestinal tumor cells. The purpose of this systemic review was to highlight the possible role of gut bacterial vesicles in the development, progression, and pathogenesis of gastrointestinal tract cancer and their possible involvement in the modulation of the tumor microenvironment. An infinitesimal amount of research has been carried out on the impact of bacterial extracellular vesicles on oncogenesis and tumor progression. This review aimed to encourage more investigations on this subject.Bacterial extracellular vesicles are membrane-enclosed, lipid bi-layer nanostructures that carry different classes of biomolecules, such as nucleic acids, lipids, proteins, and diverse types of small molecular metabolites, as their cargo. Almost all of the bacteria in the gut secrete extracellular vesicles to assist them in competition, survival, material exchange, host immune modulation, infection, and invasion. The role of gut microbiota in the development, progression, and pathogenesis of gastrointestinal tract (GIT) cancer has been well documented. However, the possible involvement of bacterial extracellular vesicles (bEVs) in GIT cancer pathophysiology has not been given due attention. Studies have illustrated the ability of bEVs to cross physiological barriers, selectively accumulate near tumor cells, and possibly alter the tumor microenvironment (TME). A systematic search of original published works related to bacterial extracellular vesicles on gastrointestinal cancer was performed for this review. The current systemic review outlines the possible impact of gut microbiota derived bEVs in GIT cancer in light of present-day understanding. The necessity of using advanced sequencing technologies, such as genetic, proteomic, and metabolomic investigation methodologies, to facilitate an understanding of the interrelationship between cancer-associated bacterial vesicles and gastrointestinal cancer is also emphasized. We further discuss the clinical and pharmaceutical potential of bEVs, along with future efforts needed to understand the mechanism of interaction of bEVs in GIT cancer pathogenesis.
  • Talman, Virpi; Provenzani, Riccardo; af Gennäs, Gustav Boije; Tuominen, Raimo K.; Yli-Kauhaluoma, Jari (2014)
  • Asghar, Muhammad Yasir; Lassila, Taru; Törnquist, Kid (2021)
    Calcium signaling participates in a vast number of cellular processes, ranging from the regulation of muscle contraction, cell proliferation, and mitochondrial function, to the regulation of the membrane potential in cells. The actions of calcium signaling are, thus, of great physiological significance for the normal functioning of our cells. However, many of the processes that are regulated by calcium, including cell movement and proliferation, are important in the progression of cancer. In the normal thyroid, calcium signaling plays an important role, and evidence is also being gathered showing that calcium signaling participates in the progression of thyroid cancer. This review will summarize what we know in regard to calcium signaling in the normal thyroid as, well as in thyroid cancer.
  • Young, T. Kue; Kelly, Janet J.; Friborg, Jeppe; Soininen, Leena; Wong, Kai O. (2016)
    Objectives. To determine and compare the incidence of cancer among the 8 Arctic States and their northern regions, with special focus on 3 cross-national indigenous groups - Inuit, Athabaskan Indians and Sami. Methods. Data were extracted from national and regional statistical agencies and cancer registries, with direct age-standardization of rates to the world standard population. For comparison, the "world average'' rates as reported in the GLOBOCAN database were used. Findings. Age-standardized incidence rates by cancer sites were computed for the 8 Arctic States and 20 of their northern regions, averaged over the decade 2000 - 2009. Cancer of the lung and colon/rectum in both sexes are the commonest in most populations. We combined the Inuit from Alaska, Northwest Territories, Nunavut and Greenland into a "Circumpolar Inuit'' group and tracked cancer trends over four 5-year periods from 1989 to 2008. There has been marked increase in lung, colorectal and female breast cancers, while cervical cancer has declined. Compared to the GLOBOCAN world average, Inuit are at extreme high risk for lung and colorectal cancer, and also certain rare cancers such as nasopharyngeal cancer. Athabaskans (from Alaska and Northwest Territories) share some similarities with the Inuit but they are at higher risk for prostate and breast cancer relative to the world average. Among the Sami, published data from 3 cohorts in Norway, Sweden and Finland show generally lower risk of cancer than non-Sami. Conclusions. Cancer among certain indigenous people in the Arctic is an increasing public health concern, especially lung and colorectal cancer.
  • Woock, Malin; Martinez-Majander, Nicolas; Seiffge, David J.; Selvik, Henriette Aurora; Nordanstig, Annika; Redfors, Petra; Lindgren, Erik; Sanchez van Kammen, Mayte; Rentzos, Alexandros; Coutinho, Jonathan M.; Doyle, Karen; Naess, Halvor; Putaala, Jukka; Jood, Katarina; Tatlisumak, Turgut (2022)
    The association between stroke and cancer is well-established. Because of an aging population and longer survival rates, the frequency of synchronous stroke and cancer will become even more common. Different pathophysiologic mechanisms have been proposed how cancer or cancer treatment directly or via coagulation disturbances can mediate stroke. Increased serum levels of D-dimer, fibrin degradation products, and CRP are more often seen in stroke with concomitant cancer, and the clot retrieved during thrombectomy has a more fibrin- and platelet-rich constitution compared with that of atherosclerotic etiology. Multiple infarctions are more common in patients with active cancer compared with those without a cancer diagnosis. New MRI techniques may help in detecting typical patterns seen in the presence of a concomitant cancer. In ischemic stroke patients, a newly published cancer probability score can help clinicians in their decision-making when to suspect an underlying malignancy in a stroke patient and to start cancer-screening studies. Treating stroke patients with synchronous cancer can be a delicate matter. Limited evidence suggests that administration of intravenous thrombolysis appears safe in non-axial intracranial and non-metastatic cancer patients. Endovascular thrombectomy is probably rather safe in these patients, but probably futile in most patients placed on palliative care due to their advanced disease. In this topical review, we discuss the epidemiology, pathophysiology, and prognosis of ischemic and hemorrhagic strokes as well as cerebral venous thrombosis and concomitant cancer. We further summarize the current evidence on acute management and secondary preventive therapy.
  • Chabok, A; Thorisson, A; Nikberg, M; Schultz, JK; Sallinen, V (2021)
    Left-sided colonic diverticulitis is a common condition with significant morbidity and health care costs in Western countries. Acute uncomplicated diverticulitis which is characterized by the absence of organ dysfunction, abscesses, fistula, or perforations accounts for around 80% of the cases. In the last decades, several traditional paradigms in the management of acute uncomplicated diverticulitis have been replaced by evidence-based routines. This review provides a comprehensive evidence-based and clinical-oriented overview of up-to-date diagnostics with computer tomography, non-antibiotic treatment, outpatient treatment, and surgical strategies as well as follow-up of patients with acute uncomplicated diverticulitis.
  • Raivola, Juuli; Haikarainen, Teemu; Silvennoinen, Olli (2020)
    The Janus kinase-signal transducer and activator of transcription protein (JAK-STAT) pathway mediates essential biological functions from immune responses to haematopoiesis. Deregulated JAK-STAT signaling causes myeloproliferative neoplasms, leukaemia, and lymphomas, as well as autoimmune diseases. Thereby JAKs have gained significant relevance as therapeutic targets. However, there is still a clinical need for better JAK inhibitors and novel strategies targeting regions outside the conserved kinase domain have gained interest. In-depth knowledge about the molecular details of JAK activation is required. For example, whether the function and regulation between receptors is conserved remains an open question. We used JAK-deficient cell-lines and structure-based mutagenesis to study the function of JAK1 and its pseudokinase domain (JH2) in cytokine signaling pathways that employ JAK1 with different JAK heterodimerization partner. In interleukin-2 (IL-2)-induced STAT5 activation JAK1 was dominant over JAK3 but in interferon-gamma (IFN gamma) and interferon-alpha (IFN alpha) signaling both JAK1 and heteromeric partner JAK2 or TYK2 were both indispensable for STAT1 activation. Moreover, IL-2 signaling was strictly dependent on both JAK1 JH1 and JH2 but in IFN gamma signaling JAK1 JH2 rather than kinase activity was required for STAT1 activation. To investigate the regulatory function, we focused on two allosteric regions in JAK1 JH2, the ATP-binding pocket and the alpha C-helix. Mutating L633 at the alpha C reduced basal and cytokine induced activation of STAT in both JAK1 wild-type (WT) and constitutively activated mutant backgrounds. Moreover, biochemical characterization and comparison of JH2s let us depict differences in the JH2 ATP-binding and strengthen the hypothesis that de-stabilization of the domain disturbs the regulatory JH1-JH2 interaction. Collectively, our results bring mechanistic understanding about the function of JAK1 in different receptor complexes that likely have relevance for the design of specific JAK modulators.
  • Mäki, Toni (Helsingin yliopisto, 2020)
    The human immune system can provide a powerful tool in developing therapies against various cancers. Even though the idea of an immune system actively searching for and disposing of potential mutated tumor cells is over a century old, only recent developments in various fields such as mass spectrometry, immuno-checkpoint blockade strategies and in silico modelling have enabled the realization of the full potential of recruiting immune system to fight cancer and the possibilities of personalized therapies. These therapeutic methods, including but not limited to oncolytic virus therapies, T-cell therapies and cancer vaccines, are based on the body’s ability to recognize mutated antigen peptides presented on the cell surface by MCH-receptors (also known as HLA-receptors in humans) and the disposal of the malignant cells by cytotoxic T-cells. Thus, the capability to map the individual HLA-presented peptidome and differentiate the immunogenic peptides is a foundation for this plethora of therapies and is in focus of ongoing research. This master thesis is a part of a project aiming to set up immunoaffinity-purification/MS based method in order to analyse the ligandome and determine T-cell recognized cancer associated antigens from tumor cells. Objectives of the work: 1. Characterizing tumor cell lines. 2. Immunological assay set up. 3. Collecting cell culture material for the ligandome affinity purification. 4. In silico prediction if the immunogenicity of selected peptides and assessing their source proteins. Methods used: 1. Cell culture. 2. FACS-analysis. 3. MTS-viability assay. 4. Immunological assays (ELISA, ELISPOT). 5. Immunological bioinformatics analysis tools (IEDB) and database search (UniPROT). Results: 1. Flow cytometric analysis provided essential information of the cell line HLA-1 expression. Additional information of PD-L1 expression can be used to evaluate cell line’s immune-evasion abilities. Preliminary MTS assay is used to determine linear range and optimal time frame for the PBMC/cancer cell co-culture killing assay. 2. Interferon γ cytokine secretion was determined by ELISPOT to assess PBMC response against known antigens in a preliminary experiment to approximate usable range for the following antigen specific PBMC assays. ELISA is used to confirm the presence of HLA-I receptors in the ligandome affinity purification eluates and to estimate the efficacy of purification. 3. Feasibility of in silico methods in the prediction of immunogenic peptides was explored. The experiments provided information that can be applied to the further development of the immune ligandome discovery project. In silico methods were successfully used to characterize previously identified HLA-restricted peptides and one previously identified immunogenic T-cell epitope. Even if the data acquired in silico can be considered only nominally verified at this stage, the results are encouraging.
  • Tiusanen, Ville (Helsingin yliopisto, 2021)
    Enhancers are important regulatory elements of DNA, that are bound by transcription factors (TFs) to regulate gene expression. Enhancers control cell type specific gene expression and they can form structures called super-enhancers, that consist of multiple normal enhancers and are bound by high numbers and variety of transcription factors. These super-enhancers are important for defining cell identity and changes in the super-enhancer landscape have been linked to different cancers. In this project, characterization of super-enhancers and their transcription factors composition between primary and cancer cells were studied using genome-wide next-generation sequencing data from multiple assays, such as ChIP-seq, RNA-seq and ATAC-seq. The focus of the project was on the data processing and analysis to identify and characterize the super-enhancers. Analyses included GSEA, heatmap binding analysis, peak and super-enhancer calling and IGV analysis. This project used pancreatic HPDE cell line for primary cells and different cancers with endodermal origin as cancer cell lines. The goal of the thesis was to try show characteristic features of super-enhancers and their features in normal and cancer cells. Data analysis showed that distinct super-enhancers can be identified in cancer cells and defined super-enhancers had typical strong binding for specific transcription factor and histone modification such as histone 3 lysine 27 acetylation (H3K27ac) mark of active enhancers. Super-enhancer regions were located in highly accessible chromatin regions of the genome, and genes that were associated with HPDE super-enhancers could be shown to have association with cell identity. Peak and super-enhancer calling counts varied between cell lines for transcription factors, histone modifications and super-enhancers. Visualization of super-enhancers was successful and could show transcription factor binding and active enhancers that establish the super-enhancer structure. Comprehensive analyses allowed us to characterize typical features of super-enhancers and show differences in the numbers of super-enhancers between primary and cancer cell lines and cancer cell lines of different organ types. Analysis of the transcription factor binding showed unique peaks on some of the super-enhancers, and these peaks might have a role in inducing the super-enhancer structure.
  • Laulumaa, Saara; Varjosalo, Markku (2021)
    Commander complex is a 16-protein complex that plays multiple roles in various intracellular events in endosomal cargo and in the regulation of cell homeostasis, cell cycle and immune response. It consists of COMMD1-10, CCDC22, CCDC93, DENND10, VPS26C, VPS29, and VPS35L. These proteins are expressed ubiquitously in the human body, and they have been linked to diseases including Wilson's disease, atherosclerosis, and several types of cancer. In this review we describe the function of the commander complex in endosomal cargo and summarize the individual known roles of COMMD proteins in cell signaling and cancer. It becomes evident that commander complex might be a much more important player in intracellular regulation than we currently understand, and more systematic research on the role of commander complex is required.